Automatic cell counting provides an effective tool for medical research and diagnosis. Currently, cell counting can be completed by transmitted-light microscope, however, it requires expert knowledge and the counting accuracy which is unsatisfied for overlapped cells. Further, the image-translation-based detection method has been proposed and the potential has been shown to accomplish cell counting from transmitted-light microscope, automatically and effectively. In this work, a new deep-learning (DL)-based two-stage detection method (cGAN-YOLO) is designed to further enhance the performance of cell counting, which is achieved by combining a DL-based fluorescent image translation model and a DL-based cell detection model. The various results show that cGAN-YOLO can effectively detect and count some different types of cells from the acquired transmitted-light microscope images. Compared with the previously reported YOLO-based one-stage detection method, high recognition accuracy (RA) is achieved by the cGAN-YOLO method, with an improvement of 29.80%. Furthermore, we can also observe that cGAN-YOLO obtains an improvement of 12.11% in RA compared with the previously reported image-translation-based detection method. In a word, cGAN-YOLO makes it possible to implement cell counting directly from the experimental acquired transmitted-light microscopy images with high flexibility and performance, which extends the applicability in clinical research.